Stieleria varia sp. nov., isolated from wood particles in the Baltic Sea, constitutes a novel species in the family Pirellulaceae within the phylum Planctomycetes

Species belonging to the bacterial phylum Planctomycetes are ubiquitous members of the microbial communities in aquatic environments and are frequently isolated from various biotic and abiotic surfaces in marine and limnic water bodies. Planctomycetes have large genomes of up to 12.4 Mb, follow complex lifestyles and display an uncommon cell biology; features which motivate the investigation of members of this phylum in greater detail. As a contribution to the current collection of axenic cultures of Planctomycetes, we here describe strain Pla52$^{T}$ isolated from wood particles in the Baltic Sea. Phylogenetic analysis places the strain in the family Pirellulaceae and suggests two species of the recently described genus Stieleria as current closest neighbours. Strain Pla52$^{T}$ shows typical features of members of the class Planctomycetia, including division by polar budding and the presence of crateriform structures. Colonies of strain Pla52$^{T}$ have a light orange colour, which is an unusual pigmentation compared to the majority of members in the phylum, which show either a pink to red pigmentation or entirely lack pigmentation. Optimal growth of strain Pla52$^{T}$ at 33 °C and pH 7.5 indicates a mesophilic (i.e. with optimal growth between 20 and 45 °C) and neutrophilic growth profile. The strain is an aerobic heterotroph with motile daughter cells. Its genome has a size of 9.6 Mb and a G + C content of 56.0%. Polyphasic analyses justify delineation of the strain from described species within the genus Stieleria. Therefore, we conclude that strain Pla52$^{T}$ = LMG 29463$^{T}$ = VKM B-3447$^{T}$ should be classified as the type strain of a novel species, for which we propose the name Stieleria varia sp. nov

The structure of CgnJ, a domain of unknown function protein from the crocagin gene cluster

Natural products often contain interesting new chemical entities that are introduced into the structure of a compound by the enzymatic machinery of the producing organism. The recently described crocagins are novel polycyclic peptides which belong to the class of ribosomally synthesized and post translationally modified peptide natural products. They have been shown to bind to the conserved prokaryotic carbon storage regulator A in vitro. In efforts to understand crocagin biosynthesis, the putative biosynthetic genes were expressed and purified. Here, the first crystal structure of a protein from the crocagin biosynthetic gene cluster, CgnJ, a domain of unknown function protein, is reported. Possible functions of this protein were explored by structural and sequence homology analyses. Even though the sequence homology to proteins in the Protein Data Bank is low, the protein shows significant structural homology to a protein with known function within the competency system of Bacillus subtilis, ComJ, leading to the hypothesis of a similar role of the protein within the producing organis

Simplicilones A and B Isolated from the Endophytic Fungus Simplicillium subtropicum SPC3

Two new tetracyclic polyketides with a spirocenter, simplicilones A (1) and B (2) were isolated from the broth-culture of the endophytic fungus Simplicilliumsubtropicum (SPC3) in the course of our screening for new bioactive secondary metabolites. This endophytoic fungus is naturally harboured in the fresh bark of the Cameroonian medicinal plant Duguetia staudtii (Engl. and Diels) Chatrou. The planar structures of the simplicilones were elucidated by MS and 1D as well as 2D NMR spectroscopic techniques. The relative configuration was assigned by NOESY experiments in conjunction with coupling constants; subsequently, the absolute configurations were assigned by the modified Mosher’s method. The compounds showed weak cytotoxic effects against the cell line KB3.1 (in vitro cytotoxicity (IC50) = 25 µg/mL for 1, 29 µg/mL for 2), but were inactive against the tested Gram-positive and Gram-negative bacteria as well as fungi

Simplicilones A and B Isolated from the Endophytic Fungus SPC3.

Two new tetracyclic polyketides with a spirocenter, simplicilones A (1) and B (2) were isolated from the broth-culture of the endophytic fungus Simplicilliumsubtropicum (SPC3) in the course of our screening for new bioactive secondary metabolites. This endophytoic fungus is naturally harboured in the fresh bark of the Cameroonian medicinal plant Duguetia staudtii (Engl. and Diels) Chatrou. The planar structures of the simplicilones were elucidated by MS and 1D as well as 2D NMR spectroscopic techniques. The relative configuration was assigned by NOESY experiments in conjunction with coupling constants; subsequently, the absolute configurations were assigned by the modified Mosher's method. The compounds showed weak cytotoxic effects against the cell line KB3.1 (in vitro cytotoxicity (IC50) = 25 µg/mL for 1, 29 µg/mL for 2), but were inactive against the tested Gram-positive and Gram-negative bacteria as well as fungi

New terpenoids from the fermentation broth of the edible mushroom Cyclocybe aegerita

The strophariaceous basidiomycete Cyclocybe aegerita (synonyms Agrocybe aegerita and A. cylindracea) is one of the most praised cultivated edible mushrooms and is being cultivated at large scale for food production. Furthermore, the fungus serves as a model organism to study fruiting body formation and the production of secondary metabolites during the life cycle of Basidiomycota. By studying the secondary metabolite profiles of C. aegerita, we found several terpenoids in submerged cultures. Aside from the main metabolite, bovistol (1), two new bovistol derivatives B and C (2, 3) and pasteurestin C as a new protoilludane (4) were isolated by preparative HPLC. Their structures were elucidated by mass spectrometry and NMR spectroscopy. The relative configurations of 2-4 were assigned by ROESY correlations, and 3JH,H coupling constants in the case of 4. Applying quantitative PCR for gene expression validation, we linked the production of bovistol and its derivatives to the respective biosynthesis gene clusters

Planctomycetes bacterium strain Pla52n 16S ribosomal RNA gene, partial sequence

Isolation of strain Pla52nT and cultivation Strain Pla52nT was isolated from wood particles placed in an incubator and stored for two weeks (August–September 2014) at a depth of 2 m in the Baltic Sea, below a landing stage at Heiligendamm (‘Seebrücke Heiligendamm’, 54.146 N 11.843 E) (Oberbeckmann et al. 2018). In the laboratory, biofilms formed on the wood particles were removed by incubation with β-galactosidase (2 mg/mL, 30 °C, pH 4.7) for 30 min and subsequent sonication for 10 min at 30 °C. M1 medium buffered with 4-(2-hydroxyethyl)-1-piperazineethanesulfonic acid (HEPES) and supplemented with N-acetyl glucosamine (NAG) and artificial seawater (ASW) (designated M1H NAG ASW medium) (Boersma et al. 2019) was used for the cultivation. The medium was solidified with 8 g/L gellan gum and additionally supplemented with 500 mg/L streptomycin, 100 mg/L ampicillin and 20 mg/L cycloheximide. The cell suspension obtained after sonication was streaked on an M1H NAG ASW plate, incubated at 20 °C for six weeks and regularly checked for the presence of colonies. Colonies obtained were then subjected to 16S rRNA gene amplification and sequencing according to a previously published protocol (Rast et al. 2017). This step was included to check whether strains are members of the phylum Planctomycetes. Colonies of strains confirmed as members of the phylum Planctomycetes were re-streaked on M1H NAG ASW plates, which then served as a source for the inoculation of liquid cultures in M1H NAG ASW medium. After several days of cultivation, exponentially growing cells were used for subsequent cultivation experiments. Determination of the pH optimum for growth was performed by cultivation of strain Pla52nT in M1H NAG ASW at 28 °C with 100 mM of the following buffers: 2-(N-morpholino)ethanesulfonic acid (MES) for pH 5.0-6.5, HEPES for pH 7.0-8.0, 3-(4-(2-hydroxyethyl)piperazin-1-yl)propane-1-sulfonic acid (HEPPS) for pH 8.0 and N-cyclohexyl-2-aminoethanesulfonic acid (CHES) for pH 9.0-10.0. Cultivations for determination of the temperature optimum for growth were performed in M1H NAG ASW medium at pH 7.5. Growth of the strain was measured as optical density at 600 nm (OD600). Maximal growth rates µmax were obtained by determination of the slope in the plot of the natural logarithmic function of average OD600 values from biological triplicates against the cultivation time. The slope from at least five data points in the exponential growth phase was used as growth rate µmax (in h−1). The generation time td (in h) was calculated using the equation td = ln(2)/µmax. Microscopy Microscopic analyses included phase contrast light microscopy and field emission scanning electron microscopy (SEM) and were performed as previously described (Boersma et al. 2019). Genome information and antiSMASH analysis Sequencing of the genome of strain Pla52nT was conducted as part of a previous study (Wiegand et al. 2020). Genome and 16S rRNA gene sequence of strain Pla52nT are available from GenBank under accession numbers GCA_007860045 and MK554582, respectively. Analysis of secondary metabolite-associated gene clusters was performed using antiSMASH bacterial version 5.1.2 with relaxed strictness and the following extra features enabled: KnownClusterBlast, ActiveSiteFinder and SubClusterBlast (Blin et al. 2019)

Two xanthones and two rotameric (3⟶8) biflavonoids from the Cameroonian medicinal plant Allanblackia floribunda Oliv. (Guttiferae)

Two xanthones, 2-(3-hydroxy-3,3-dimethyldihydroallyl)-dihydro-6-deoxyisojacareubin (1) and dihydro-6-deoxyjacareubin (2), and two 3 ⟶ 8 rotameric biflavonoids, (2R,3S)-volkensiflavone-7-O-β-acetylglucopyranoside (3) and (2S,3S)-morelloflavone-7-O-β-acetylglucopyranoside (4), together with fifteen known compounds, were isolated from a dichloromethane/methanol (1:1, v/v) extract of the bark of the plant Allanblackia floribunda. The structures of the new compounds were elucidated by NMR spectroscopy and mass spectroscopic techniques and those of the known ones were deduced by comparison with data reported in the literature. The isolated biflavonoids were obtained as mixtures of conformers exhibiting duplicate NMR signals in solution at 25 °C and their respective absolute configurations were assigned using circular dichroism spectroscopy. Selected isolated compounds were assessed for their antibacterial and antioxidant propertie

Planctomycetes bacterium - Genome sequencing and assembly

Bacterial communication mostly relies on homoserine lactone molecules, while unknown species of the human microbiome employ N-acyl amino acids for cross-kingdom interaction with their host. Here we describe an unprecedented bacterium of the maverick phylum Planctomycetes which produces a novel type of N-acyl amino acids as quorum sensing signals